I couldn't find a way to call a script (shell or php) in the documentation, so I guess we have to rewrite scripts for Installatron using internal commands such as chmod, chown, etc., but what would be the best way to patch applications via the patch command?

OlivierinterfaSysWeb, mobile, hosting product and service development experts

Have you given some thoughts about allowing users to easily patch the apps? Not sure how popular this would be as only advanced users would want to automatically customize their apps.
Each app could have an optional patch file being applied to it and there would need to be a dry run first.

OlivierinterfaSysWeb, mobile, hosting product and service development experts